Trial lawyers have a saying, "When the law isn't on your side, argue the facts." That's what The New York Times did in early October when it made its case—through five lengthy articles and a capstone editorial—for curbing the rights of religious organizations. Its examples of religious freedom run amok were all perfectly legal, but morally questionable.

One of the newspaper's examples: A Roman Catholic order in Toledo dismissed Mary Rosati after finding she'd been diagnosed with breast cancer. Rosati claimed the order wanted to avoid the expense of caring for her. The religious order countered that it found Rosati unqualified for its way of life. Since questions of theology and spiritual calling were invoked, a district judge in Ohio dismissed Rosati's complaint.

The Times's not-so-subtle editorial-page conclusion: "The wall between church and state is being replaced by a platform that raises religious organizations to a higher legal plane than their secular counterparts." In other words, religion is taking over, while "the majority [of Americans] is not aware."

But Times editors misunderstand the basic notions embedded in the First Amendment. "Congress shall make no law respecting an establishment of religion," our foremost right reads, "or prohibiting the free exercise thereof." The first clause forbids elevating one religious group over another. The second allows such groups free rein over their own affairs.

Congregations receive tax exemptions, not because of the public service they offer—social workers, inner-city teachers, and employees at secular nonprofits all benefit the common good while still paying taxes—but mainly because the power to tax is the power to manipulate, control, or even destroy. ...